CD-HIT can be used for clustering large sequence sets  or  removing identical or highly similar sequences from a sequence set. CD-HIT is often used as a tool to produce a non redundant sequence set for further analysis of a large sequence set. CD-HIT recognizes fasta and fastq sequence formats.


Version on CSC's Servers

Taito: 4.6.8


The setup command for CD-HIT in Taito cluster is:

module load biokit

After the setup command, the server recognizes CD-HIT commands. The CD-HIT package has many programs. The most notable are:

Program Description
cdhit Clustering and redundance removal tool for protein sequences
cdhit-est Clustering and redundance removal tool for nucleic acid sequences (only for sequences that do not contain introns)
cdhit-2d Tool to compare two protein sequence sets
cdhit-est-2d Tool to compare two nucleic sequence sets
cdhit-454 A program to identify artificial duplicates from raw 454 sequencing reads


A ful list of programs can be found in the CD-HIT user guide.

You can list the command line options of CD-HIT programs by using option -help. For example:

cd-hit -help

A simple analysis for a protein sequence set can be done for example with command:

cd-hit -i my_proteins.fasta -o reduced_set.fasta -c 0.95

The sample command above produces two result files:

  1. reduced_set.fasta contains a pruned sequence set. In this case, if two sequences are more than 95% identical, only the longer one is included to the results.
  2. reduced_set.fasta.clstr contains information about the clustering of the sequences that share higher similarity than the give threshold value (in this case 95%).




For citations please see CD-HIT documentation.



CD-HIT user guide

CD-HIT home page